5L2W

The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W98 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP286.15PEG20K, 180mM Mg(HCO2)2, 0.1M MES pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.7355.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.307α = 90
b = 100.307β = 90
c = 151.857γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98.15PIXELDECTRIS PILATUS3 S 6M2015-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.84599.922.912.7619770100.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1W982.8451974196299.990.20190.19950.2463RANDOM84.34
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-6.1078-6.107812.2156
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.34
t_omega_torsion2.72
t_angle_deg1.15
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.34
t_omega_torsion2.72
t_angle_deg1.15
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4608
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms35

Software

Software
Software NamePurpose
BUSTERrefinement
autoXDSdata processing
BUSTERphasing
Aimlessdata scaling